♻️ Refactor EquivalenceCheckingManager and 📝✨ Revamp Documentation

[burgholzer]

Description

This pull request includes several enhancements and updates across the project and associated documentation:

1. Updated dependencies such as mqt-core and pre-commit hooks to their latest versions.
2. Refactored EquivalenceCheckingManager to streamline its public interface by removing redundant methods.
3. Modernized project documentation and added a citation file for referencing.
4. Improved the structure of Python tests and slightly revamped the Python package with better documentation.
5. Adjusted Python bindings by moving documentation to stubs and refined counterexample handling for better flexibility.
6. Incorporated smaller code quality improvements.
7. Updated the Read the Docs (RtD) build configuration.

This contains some breaking changes on the C++ as well as the Python side. However, these should simplify the usage of the library and generally reduce the size of the code base. With the 3.0 release coming up, this is the time for making such changes.

At least locally, it also looks like this will fix #546. That still needs to be verified though.

Checklist:

• The pull request only contains commits that are related to it.
• I have added appropriate tests and documentation.
• I have made sure that all CI jobs on GitHub pass.
• The pull request introduces no new warnings and follows the project's style guidelines

[codecov]

Codecov Report

Attention: Patch coverage is 98.41270% with 1 line in your changes missing coverage. Please review.

Project coverage is 96.0%. Comparing base (0fc699b) to head (35cf328).
Report is 24 commits behind head on main.

Files with missing lines	Patch %	Lines
src/checker/dd/simulation/StateGenerator.cpp	75.0%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##            main    #566     +/-   ##
=======================================
- Coverage   96.1%   96.0%   -0.2%     
=======================================
  Files         40      38      -2     
  Lines       1877    1721    -156     
  Branches     224     197     -27     
=======================================
- Hits        1805    1653    -152     
+ Misses        72      68      -4     

Flag	Coverage Δ
cpp	95.4% <97.9%> (-0.7%)	⬇️
python	97.7% <100.0%> (+1.2%)	⬆️

Files with missing lines	Coverage Δ
include/Configuration.hpp	75.0% <100.0%> (+8.3%)	⬆️
include/EquivalenceCheckingManager.hpp	100.0% <100.0%> (ø)
include/checker/dd/DDSimulationChecker.hpp	100.0% <100.0%> (ø)
include/checker/zx/ZXChecker.hpp	100.0% <100.0%> (ø)
src/Configuration.cpp	100.0% <100.0%> (ø)
src/EquivalenceCheckingManager.cpp	92.6% <100.0%> (-0.4%)	⬇️
src/mqt/qcec/__init__.py	100.0% <ø> (ø)
src/mqt/qcec/_compat/optional.py	100.0% <ø> (ø)
src/mqt/qcec/compilation_flow_profiles.py	98.1% <100.0%> (+<0.1%)	⬆️
src/mqt/qcec/configuration.py	100.0% <100.0%> (ø)
... and 4 more

... and 3 files with indirect coverage changes

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